1. How to bioengineer a novel system? Obtain a sequence by PCR, then clone it into a suitable plasmid We’re adding DNA, but want E. coli to make a protein!

2. 1)In bacteria transcription and translation are initially coupled

3. 1)In Bacteria transcription and translation are initially coupled RNA polymerase quits if ribosomes lag too much

4. 1)In Bacteria transcription and translation are initially coupled RNA polymerase quits if ribosomes lag too much Recent studies show that ribosomes continue translating once mRNA is complete; i.e after transcription is done

5. Bacteria have > 1 protein/mRNA (polycistronic) http://bmb-it- services.bmb.psu.edu/bryant/lab/Project/Hydrogen/index.html#secti on1 euk have 1 protein/mRNA

6. Bacteria have > 1 protein/mRNA (polycistronic) Mutations can have polar effects: mutations in upstream genes may affect expression of perfectly good downstream genes!

7. Regulating transcription Telling RNA pol to copy a DNA sequence

8. Regulating transcription Telling RNA pol to copy a DNA sequence Transcription factors bind promoters & control initiation of transcription

9. Regulating transcription Telling RNA pol to copy a DNA sequence Transcription factors bind promoters & control initiation of transcription 1/signal gene senses

10. Regulating transcription Telling RNA pol to copy a DNA sequence Transcription factors bind promoters & control initiation of transcription 1/signal gene senses 1 binding site/signal gene senses

11. Transcription factors Bind surface -> base-pairs form unique patterns in major & minor grooves

12. Transcription factors Bind surface -> base-pairs form unique patterns in major & minor grooves Scan DNA for correct pattern

13. Transcription factors Bind surface -> base-pairs form unique patterns in major & minor grooves Scan DNA for correct pattern need 15 - 20 H-bonds = 5-8 base-pairs

14. Transcription Prokaryotes have one RNA polymerase makes all RNA core polymerase = complex of 5 subunits (      ’  )

15. Transcription Prokaryotes have one RNA polymerase makes all RNA core polymerase = complex of 5 subunits (      ’  )  not absolutely needed, but cells lacking  are very sick

16. Initiating transcription in Prokaryotes 1) Core RNA polymerase is promiscuous

17. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity

18. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity Bind promoters

19. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity Bind promoters Different sigmas bind different promoters

20. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity Bind promoters 3) Once bound, RNA polymerase “melts” the DNA

21. Initiating transcription in Prokaryotes 3) Once bound, RNA polymerase “melts” the DNA 4) rNTPs bind template

22. Initiating transcription in Prokaryotes 3) Once bound, RNA polymerase “melts” the DNA 4) rNTPs bind template 5) RNA polymerase catalyzes phosphodiester bonds, melts and unwinds template

23. Initiating transcription in Prokaryotes 3) Once bound, RNA polymerase “melts” the DNA 4) rNTPs bind template 5) RNA polymerase catalyzes phosphodiester bonds, melts and unwinds template 6) sigma falls off after ~10 bases are added

24. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5’ to transcription start) 5’-TATAAT-3’ determines exact start site: bound by  factor

25. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor

26. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor 3) UP element : -57: bound by  factor

27. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor 3) UP element : -57: bound by  factor

28. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor 3) UP element : -57: bound by  factor Other sequences also often influence transcription! Eg Trp operator

29. Prok gene regulation 5 genes (trp operon) encode trp enzymes

30. Prok gene regulation Copy genes when no trp Repressor stops operon if [trp]

31. Prok gene regulation Repressor stops operon if [trp] trp allosterically regulates repressor can't bind operator until 2 trp bind

32. lac operon Some operons use combined “on” & “off” switches E.g. E. coli lac operon Encodes enzymes to use lactose lac Z =  -galactosidase lac Y= lactose permease lac A = transacetylase

33. lac operon Make these enzymes only if: 1) - glucose

34. lac operon Make these enzymes only if: 1) - glucose 2) + lactose

35. lac operon Regulated by 2 proteins 1) CAP protein : senses [glucose]

36. lac operon Regulated by 2 proteins 1)CAP protein : senses [glucose] 2)lac repressor: senses [lactose]

37. lac operon Regulated by 2 proteins 1)CAP protein : senses [glucose] 2)lac repressor: senses [lactose] encoded by lac i gene Always on

38. lac operon 2 proteins = 2 binding sites 1) CAP site: promoter isn’t active until CAP binds

39. lac operon 2 proteins = 2 binding sites 1)CAP site: promoter isn’t active until CAP binds 2)Operator: repressor blocks transcription

40. lac operon Regulated by 2 proteins 1) CAP only binds if no glucose -> no activation

41. lac operon Regulated by 2 proteins 1) CAP only binds if no glucose -> no activation 2) Repressor blocks transcription if no lactose

42. lac operon Regulated by 2 proteins 1) CAP only binds if no glucose 2) Repressor blocks transcription if no lactose 3) Result: only make enzymes for using lactose if lactose is present and glucose is not

44. Result [  -galactosidase] rapidly rises if no glucose & lactose is present W/in 10 minutes is 6% of total protein!